The sixth great village
by ceasare
Summary: Danzo uses Kotoamatsukami on the Daimyo and becomes Hokage after Pain's invasion. He tries to extract the Kyuubi but Naruto's friends help him escape. He goes to Ame to seek help, but arrives during Konan's and Obito's fight. Obito dies and the Akatsuki ends with him only to be reborn through Naruto as a means of true peace instead of violence. !Rinnengan NarutoxKonan


_**A.N Welcome to my story I hope you will like to read it as much as I will like writing it! =D**_

 _ **This will be an AU fanfic the divergent is that Danzo pretty much genjutsus the Daimyo's ass and becomes Hokage**_ **does not go to the Kage meeting. Subsequently Danzo does not go to the Kage meeting and Sasuke attacks Konoha because he has the 'cool eyes of spinning death'. Sasuke dies and Danzo creates a militaristic Konoha. Tsunade gets assassinated and Konoha enters an era of darkness. Naruto is ordered to be executed and the Kyuubi to be extracted in order to be sealed inside another host. However Naruto escapes with the help of the Konoha twelve. The story starts with Naruto heading to Ame.**

 **A.E (Author's excuses): I tried... I really did try to write a prologue chapter with the whole backstory but it seemed extremely corny and shallow. I hate stories where Naruto gets banished 'just cause'. Jinchuuriki are considered as 'military' resources and are therefore extremely valuable to have in a village. The council would never banish Naruto end of story. Naruto is the nuclear bomb in 'Murica's (Don't get insulted Americans! xD) stockpile and America would never throw their nukes in the sea to let anyone pick 'em up, that's how important he is. So without doubt Naruto has to escape but he wouldn't do that unless threatened. I also hate stories where Naruto runs away due to villagers and hates them. Naruto as an ideal in Kishimoto's story is everything but hate. So I have to get him out of Konoha without the threat of him hating and destroying Konoha (Konoha as an ideal btw. not the actual place). So this is my solution to the problem, make Naruto hate Danzo but not Konoha simple right? Also I wanted Naruto to be an Akatsuki because I think that the robes and painted nails are bad ass. But he is a jinchuuriki so I can't have him hunting bijuu right? So after Obito's death he will restart the original Akatsuki.**

 **I had to give those spoilers away to explain some things without wasting four chapters of your life. These spoilers are mild and in the end they will not affect this story, I wanted to take Madara and Kaguya out of the picture and create a slightly realistic fourth shinobi war!**

 **Sorry that was me rumbling. Enjoy!**

 **P.S I will explain more with the wonder of flashback no jutsu (S rank) and add some talk no jutsu (SS-rank only 2 known shinobi could do it right!)**

 **I love Post Scriptums you just add an S right?**

Chapter 1 – Welcome to Ame!

Naruto Uzumaki almost never got tired from physical activity. As a matter of fact he could count the numbers he was exhausted with his fingers. At the moment however all he wanted was to roll under a rock and sleep for eternity. He ran for three days straight and he was sure that Gai and Lee would be praising his youthfulness if they were with him. He still couldn't come to terms with his escape. One moment he was basking with the villagers praise and a couple of days later he was to be executed. His surrogate mother Tsunade died due to extreme chakra exhaustion. Danzo didn't allow him to mourn however since the first decree was to execute him and reseal the Kyuubi into a baby that would be then stay concealed so that the Akatsuki didn't know where the Kyuubi was. During the preparations Sai came to his cell removed the chakra containing seals on Naruto and left without saying a word. When he went into Sage mode Naruto felt the explosions and disturbances that his comrades created. He assumed they were giving him a chance to escape, so he just broke through the cell and ran as fast as he could. The only safe place he could think of at the time was Ame and Konan.

Naruto entered Ame's border without being seen. It wasn't that hard in his opinion since he didn't encounter any border patrol. He sat down on a rock and entered Sage mode to feel for any people who might be in his way. He also had no idea where the hidden village itself was so he would just follow the biggest concentration of signatures. What he found though was scary. One signature was fading and it belonged to Konan and the other seemed to disappear every so often but reappearing at the same place. 'I think she's in trouble!' he took of at speeds beyond those most shinobi would expect to reach in their life. He could make out a huge explosion in the distance, he felt her signature fade faster and picked up his speed.

When Naruto arrived at the origin of the two signatures he found a man holding Konan by the neck squeezing the life out of her. He couldn't see his face but he seemed like an Akatsuki member.

Obito cast a genjutsu on Konan and quickly went through her memories to find the location of Nagato's eyes. Suddenly all he could feel was pain and for a second he was going to shrug it off but then a scream and darkness. Obito died due to **Rasengan** through his head, all dreams of domination and the eternal Tsukuyomi was destroyed. Due to an unexpected variable in Madara's calculations. Danzo had inevitably saved the world of destruction through a foolish attempt of gaining power.

Konan opened her eyes but quickly closed them because of the blinding light. 'What is this?' she thought to herself, was she dead? She slowly opened her eyes again and saw that she was in hospital room. She briefly remembered dying at Madara's hands. Her left hand felt warm but when she looked she saw a mop of blonde hair and gasped when she realized who it was. "Naruto?!". Naruto woke up and saw that Konan was awake. He broke into a wide smile and hugged her.

"I thought you were dead, 'ttebayo!" he yelled at her and let off his hug to look at her. She couldn't believe it, why was he here, what happened to Madara?

"What happened? I was sure Madara was going to kill me!" she became a little somber at that, maybe taking the guy head on was a bit of a stretch.

"Madarin?" Konan sweat dropped.

"Madara! The guy with the orange mask!" she huffed indignantly.

"Oh... I killed him" he seemed a bit sad?

"..."

'Either he is joking or I am the luckiest around'

"Explain please. Why are you in Ame anyway?"

"It's a long story, I escaped because they wanted to execute me"

"WHAT!" this time she couldn't hold it he was driving her insane. Why would Konoha want to execute the guy that saved them? However if he was telling the truth and still held his conviction then Nagato had chosen right, only time would tell.

"Chill I'll explain when you are rested but the gist of the story is that I came to Ame to seek refugee and when I came through the border I felt your chakra so I ran to you but found you dying at the hands of that Madara guy so I put a Rasengan through his head... But you did a number on him, he lacked a hand from what I could see."

Konan smiled at that, it seemed that she really was lucky to still be alive. Who knows what would happen if he got Nagato's eyes.

"What happened to his body?"

"Didn't have time to pick it up, so it's inside the lake, all I know is that he lacked arm and a head so I assume he is dead unless he's like that Hidan freak." he said with a shrug.

"Do you know who you killed! Don't act like it was a small thing!"

"huh? The guy was half dead already, you did the job I just Rasenganed his ass"

Konan then realized that the world had narrowly avoided destruction due to a twist of fate, a few seconds later she broke into a fit of laughter.

"What's so funny?"

"He was the guy who manipulated me and Nagato! Without him Akatsuki is no more!"

When Naruto heard that he smiled and laughed with her, it seems something good happened after all.

"How long was I out? How is the village?"

"The people here seemed distressed when I came here carrying you. They thought that I killed you and started attacking me for killing their 'Angel'. But then I explained and they let me stay here with you until you recuperated. It's been a week since then. I don't really know the village so I stayed here, and I didn't find any ramen stands so I assume that this village sucks." he said with a huff. Seriously how can a village not have a ramen stand! It was an insult to the gods themselves!

"So I assume you want to join Ame?"

He scratched his chin obviously trying to explain his reasoning.

"I thought about it during the week and I have to say that the village seems nice, though it rains a lot but I guess that's why it's called the village hidden in the rain. I didn't think it was that literal. But you would be troubled if Konoha found that you protect their S ranked 'weapon' " His face rested in a scowl at the end of his sentence

"Nagato used to feel all villagers through the rain so it is quite handy at times" she smirked a bit at him. His attitude was infectious and having a S rank shinobi in the village would help tremendously now that Nagato was dead, Ame was known to be secretive so no-one would find anything just yet.

"Ame is secretive and all of our shinobi know to keep their mouth shut. Besides I need someone to help me lead the village"

"Are you sure? I mean I am only sixteen"

"And already a lot wiser than expected, I wasn't made to lead you know and I have followed Nagato and Yahiko around since I was a child. I am just the public face of Ame the leader was Nagato. Nagato put his trust in you and I will do the same."

"I am honored but I really don't know if I can do it. I would have to train a lot first too"

"When Madara stabbed me he asked me why I believed in you."

"What did you say?"

"At that moment the rain stopped and I saw it clearly. I told him that you are the light that will guide us to walk through the darkness."

"Thank you Konan, I will help in anyway I can."

"What are you going to do about Konoha?"

"I have to free them from Danzo's hands and if all goes well he will have to be assassinated, I see no other way around him. He will call for war I know it. Neither Jiraya or Tsunade trusted him and I sure as hell don't trust him. For the time being though I don't know. I sent a toad to do some sniffing but he will likely take some time to respond."

"I see Nagato chose well" she s whispered to herself but Naruto heard her.

"What do you mean?"

"I expected you to go for revenge but you still try to help them." she said with a fond smile.

"I see, I will call a nurse and find me when you rest, I'll check in a hotel and we can talk later ok?

"Yes, I need time to think about everything"

"I'll see you later then"

A week had gone by since Naruto and Konan had their talk. Naruto walked through the village ofter to explore the different locations and buildings. Ame was in his opinion beautiful. The buildings were made out of metal and were quite tall. The village itself was separated in districts made out of rings. Most civilians lived in the outer rings and the shinobi training grounds were located near the Kage tower, or so Naruto called it. Amegakure didn't have a Kage because it didn't belong to the great five. However he realized that it probably should. Ame was located between the five great villages and was located in a very significant geographic location. All great shinobi wars were waged in Ame and he would have to insure that Ame would stop being the collateral if he would have to lead this place then he would make sure that everyone would be safe. Another thing he noticed was that every store had a paper angel hung outside and people were talking about Pain and Konan as if they were deities of sorts. He frowned at that thought. Nagato made them believe that he was a god and that would have to change. He was cut out of his musings when he heard a tap on his hotel room door. He tensed a little and walked to it and opened it. A young chuuni girl was waiting for him. She blushed when she saw him but didn't react further than that.

"Can I help you?"

"Naruto-sama you have been summoned by Angel-sama"

"Non of that 'sama' stuff it makes me feel old" he said with a grin and the young chuunin's face got a tinge of red that even Hinata would be proud of. He frowned, she seemed dizzy. "Are ok? You seem a bit ill."

"I. I'm. F-fine! Naruto-sama!" she all but yelled at him and ran away.

'huh? This village has some strange kunoichi' he shrugged and got ready to meet Konan. The tower wasn't really hard to find. It was at the center of the village and the tallest building in Ame. When he arrived he was greeted by a couple of gennin who gave him an Akatsuki attire and told him that Konan requested that he wear that. He didn't really know how to feel about that but he thought that the attire _did_ look cool and decided to try it. After he changed into it he realized that he lacked all sorts of orange but the red clouds did compensate a bit. He arrived at the top and Konan was already waiting for him infront of the office door.

"I should say that this attire suits you better" she smirked at him because he looked uncomfortable.

"It lacks orange" was all he said before she ushered him inside. The office was big and it had an exit on the left that led to a metal statue that had the rinnengan eyes. Instead of a desk there were three couches set in a triangular fashion. "Why is there no desk I thought that there would at least be paperwork."

She laughed at that.

"Nagato didn't do any paperwork due to having sticks shoved into his spine and all, so it is located in my office" she snickered a bit at that thought and continued.

"This floor will be your house after all, leader" She gauged his reaction to being called a leader. He seemed a bit uneasy.

"Can you just call me Naruto? I am not a leader yet" She liked that about him, he was modest and level headed, in truth she was testing him. Most people who quickly ascended in a position of power were either swayed by others or became addicted to it. So she would have to monitor him for the time being.

"We will see about that Naruto, I don't expect you to know everything that's why I'm here after all. Sit we have a lot to discuss."

Konan started when they both sat on their respective seats.

"Tell me what happened in Konoha."

"Not much I can tell you. Danzo became Hokage and wanted to extract the Kyuubi from me. But my friends backed me up and helped me escape. I decided that coming here was the best course of action since you were the only ally I had outside of the village."

She scowled at the thought of Danzo, the man was like a cockroach.

"I see. Have you got any info from the toads?"

"The toads informed me that he set an entry in the bingo books for Uchiha Sasuke, and that there will be a Gokage meeting in Tetsu no kuni in a month" she was a bit surprised at that. There had only been two Kage meetings in history.

"Will Danzo attend?"

"No. From what I gather there is instability in Konoha and he cannot afford to leave."

"That's what I thought. Maybe we should attend and inform them of the end of Akatsuki."

"That was my thought but they will kill me if they see me enter with this cloak."

"That leads me to the second thing I wanted to talk about today which is Nagato's eyes."

"What about them?"

"They would be a waste if we destroyed them and we cannot afford to keep them intact. I hate to do this to Nagato's body but he would be happy to have them in good use"

"What are you implying?"

"I am offering them to you. With your Uzumaki lineage and the Kyuubi's chakra you could handle them far better than Nagato did. Madara told me that he implanted them in Nagato when he was a kid so I know that they weren't his to begin with."

"I don't know Konan, it would be weird"

"No disrespect but the only reason you won against the 'Six Paths of Pain' was because he couldn't use Tendo's powers due to the destruction of Konoha. With Senjutsu and your vast amounts of chakra you would be at least five times more powerful."

"I don't seek easy power Konan" he said with a calm voice.

"I know which is why I am offering the eyes to you. Trust me on this, in a month you could learn to use them at least a bit effectively and you could attend the meeting without the worry of getting attacked, it is the only way out and we can't hope to get another Kage meeting."

"I see. Are you really OK with this? "

"I wouldn't bring it up otherwise."

"It shall be done then, now to move forward explain to me how this village works and what I need to do,"

They continued through the night and Konan was a bit surprised that he seemed to grasp all the functionality she described. Unlike other villages D rank missions were handled by academy students during their last year. C ranks were for gennin squads and missions above that were for chunnin only. Internal paperwork was handled by those who failed to become gennin in the physical aspects and gennin who wanted to become medics became chunnin after completing their medical training. Naruto suggested that every chunnin squad on B ranks and above be accompanied by a medic and he surprised Konan a bit since she realized that Nagato and she were too caught up with Akatsuki business to look after their own village. All in all they discussed all sorts of aspects and protocols of the village and came up with measures and ideas for many problems that haunted Ame in the past. Naruto integrated a lot of Konoha's principles without jeopardizing the status quo of Ame.

Naruto woke up in the morning and found himself on the same couch he sat the day before. He was covered with a cloth to keep him warm and Konan wasn't there so he thought that she left sometime during the night. He walked out of the office and noticed that the apartment was actually huge, There was a big hall filled with books and scrolls which he assumed belonged to Nagato. He was inwardly jumping out of his skin with all the knowledge he could get. Although he wasn't happy about the books he knew the cheat that would push him ahead in life. "Kage bunshin no jutsu!" he inwardly smirked when ten clones appeared in a poof and started reading the material. He walked through another room to find the kitchen and another room almost as big as the office that had a huge windows overlooking Amegakure. He took in the sight before continuing on. He opened the last door and gasped when he saw the bathroom. It had a huge onsen inside that could easily be as big as his apartment back in Konoha. 'Maybe I should send Danzo a post card? Nah' he smiled a bit at that thought. He never expected life to take this turn.

He heard a sound coming from the entrance of the apartment and went to greet his visitor. What he didn't expect though was the same girl from yesterday.

"Hello!" he smiled at her and she got another blush. 'weird she may be a bit sickly' he thought to himself."Naruto-sama I have been assigned as your assistant from Angel-sama!"

He kinda liked the idea.

"What's your name assistant-san?"he said politely, she looked really kind just like Hinata.

"My name is Shizuka, Naruto-sama." she bowed lightly.

Shizuka was a girl of average height, she had black hair and green eyes. He assumed she was a kunoichi but didn't have a headband on her.

"Ok then Shizuka-san, make yourself at home I guess, I'll take a quick bath."

She nodded at him and he went on to the onsen, nothing like a good warm bath.

When he came back she was cleaning the kitchen so he went inside. She prepared a breakfast for him so he sat at the table and started eating. "Is there anything Angel-sama has to tell me?"

"Yes, she wanted you to meet her at the hospital in the afternoon"

"Today already huh?"

"Soo.. Shizuka-chan let's introduce each other a bit" he said.

"What do you mean?" she tilted her head in confussion.

"Hmm, OK I'll start I guess. I am Uzumaki Naruto, sixteen years old, I love Ramen and hate that Ame has no ramen stand." He frowned again and heard Shizuka giggle a little. "My dream is to find a way to bring peace to the world" Shizuka looked a bit awed at the last part.

"I am Shizuka, fifteen years old, I love my family and friends, I don't know if I hate anything but my dream is to become a strong kunoichi to protect my village" she finished with a smile and Naruto couldn't help but admire her goal. It was in a way very similar to his so he would help her if he could.

"You know that's really great. A good friend once told me that only when you protect something dear can you become truly strong. So I will help you as much as I can" he smiled at her and she inwardly sighed at how dreamy he looked with that spiky hair. "Thank you a lot Naruto-sama!"

He nodded at her and left to find something interesting to read in the library. He decided to let people call him whatever they wanted as long as they didn't over do things. He couldn't find it in himself to act all cheery and bubbly. These people where not biased to him and as long as they didn't view him as a god he would let them respect him. Respect didn't come cheap so he would have to earn it even if they already acted respectful.

By the afternoon his head was spinning. He found books on chakra theory and control and realized that Jiraya could have helped him a lot more. He felt a slight pang in his heart when he thought of his father figure but couldn't help but scowl when he realized that he only learned life lessons and controlling the Kyuubi during their trip. Nature manipulation came only when he tried to complete the Rasengan. He could have saved Jiraya just by being a bit more aware and knowledgeable. He promised himself to never let something like that happen again and walked into the hospital. A nurse guided him to the surgery room and left when they arrived at the door. The operation was top secret and Konan would do the transplant alone. They agreed that everybody who had seen him with his original eyes would have their memories wiped and only Shizuka would retain hers but she would be sworn to secrecy. Konan didn't like that idea but Naruto was adamant that they needed to trust their own subordinates a bit more.

"So are you ready?"

"I think I'm gonna miss my eyes"

"I promise you wont. The only change will be that you'll probably look intimidating instead of all bubbly and cute" she chuckled a little but he huffed at her response.

"I don't think I look bubbly!"

"Yeah you do.. Anyway I'm gonna knock you out unless you want to feel the pain of having your eyes extracted."

"Eh... I'd rather avoid that yeah" he scratched his head sheepishly.

"Don't scream when you wake up things are going to look different.

He didn't get to respond because she chopped at his neck and he fell unconscious.

 _ **Next day**_

Naruto woke up and he opened his eyes and looked around. Everything looked crisp to the point that he could see the individual hair on his arms. A blue tint with specks of orange was visibly flowing through his hands and he freaked out at first but then realized that he was looking at his chakra. He could feel the chakra in his eyes and it was draining constantly at his reserves but it didn't really feel exhausting more like an annoying itching on his back that he couldn't scratch. He tried cutting the chakra flow and the chakra on his arms stopped being visible. 'So it works just like an ocular jutsu then.' he realized. Back in the days he asked Sasuke how it felt activating the sharingan and he had explained the basic theory behind it.

Konan entered his room and saw that he was awake. "How are you feeling?"

"I feel as if nothing changed except that I can see chakra"

"Try imagining a weapon in your hands and push chakra into your eyes" she said. Nagato had explained most of his techniques to her so she could give him some advice. She never understood the principal behind his Naraka path and the power over life techniques but she could help him in the basics.

Naruto imagined a generic kunai and pushed chakra in his eyes, he gasped when a cylinder appeared out of his hand and he recognized it as the same weapon Pain used.

"So most of the powers work that way?" he asked.

"From what Nagato told me you should have perfect control over your chakra and I created a scroll with most techniques he used in it. Unfortunately you will have to find everything else yourself as he never explained all of his techniques."

"I see. Do you have any other information on the rinnengan?"

"From what I know is that you should have an instinctual understanding of chakra. I don't know how to explain it but you will understand when the time comes."

"Ok, I guess I have to get ready for Ame's entrance in the big league huh?" Konan chuckled a bit at that.

"I trust your judgment but don't make an enemy out of the Kages we don't have the man power to stop them, and they might feel threatened from you."

"Unfortunately I will have to put their sights on Konoha for now. I hope they don't jump the gun and destroy her, but I feel that Danzo will at least protect most of it. "

"Yes, we discussed that, but your objective for the time being is telling them that Akatsuki is under new leadership and our new objectives. Also tell the Raikage that we didn't capture the Hachibi."

"I'll keep that in mind. I'll go to the training grounds I guess." With that Naruto left her in the room and went to start with his training.

The rinnengan is truly a magnificent power to hold. Unlike the sharingan or the byakugan it didn't let you copy techniques or give you a 360 degrees of vision. It gave you understanding. The power to dissect chakra at it's building blocks and understand the foundation of the world. No wonder Nagato started thinking him self as a god. After all bringing back dead people back to life is what defines a part of godhood right? But no the truth lies in chakra. In the Academy Naruto learned that chakra is the combination of physical and spiritual energies that shinobi combine into chakra and then mold to use ninjutsu. Now he realized that the energies themselves regulated the world. The soul was the spiritual chakra and the body was the physical chakra. Many would say that the explanation was the same but it was not. Spiritual chakra remained intact after death. All experiences a person has remained in the yin part of chakra. So if you 'theoretically' could see the yin part you could manipulate it and use it. So Nagato used his yin chakra to guide the 'souls' back to their 'yang' counterpart. Gaining understanding of where the dead went and what happened to them was in a way exciting for Naruto. He now knew that in a way when people said that the dead were watching them it was literally true. The dead were all around them! And the yin chakra would mix and disperse. Only potent yin chakra would remain intact and get reincarnated.

After only three weeks Naruto got most of the jutsu in the scroll down. There were observation on other jutsu, but he didn't want to bring people back to life. Doing so would be foolish, the dead should remain as such. Even though he was thankful to Nagato for bringing the dead back he wasn't sure if he would ever try himself. His Senjutsu chakra felt different now. His eyes didn't turn into those of the toads, he got black markings around his eyelids and he could gather the energy in seconds instead of minutes as was previously. His body had adapted and he couldn't feel the drain anymore even if he kept them active all the time. However he was most happy about his chakra control. He removed the orange tints from his chakra stream and decided to create a storage in his forehead just like Tsunade had done with her kinjutsu seal on her forehead. It was the same shape and size and he made it to remind himself of her. Another thing he understood about the Kyuubi now was that it's chakra was not really malicious but extremely potent. In comparison a normal shinobi's chakra was water and the bijuu's was like sake. He would need to have a talk with the fox one of these days. In the end the extremely potent bijuu chakra flowed inside him in small doses and made his own more potent. So when he tried to control it he couldn't because its potency increased at a constant rate. His father had given him a way to become powerful but shot his control to death. Naruto almost cried when he created a one handed Rasengan. He even went into Sage mode and created a one handed Rasenshuriken. Although it did take twice the time to create.

A month later with five destroyed training grounds and many sleepless nights Naruto managed to go through most of his personal jutsu and learned Nagato's techniques to an acceptable point. Sure he couldn't use his Asura path yet or bring people back to life but he could Shinra Tensei a training ground to oblivion.

With his training 'complete' he left for the Kage meeting. He was particularly anxious about what lied ahead, and felt his head spinning with the thousands of things that could go wrong. He had a bad feeling about what was coming. Danzo would not sit still and let Konoha plunge into anarchy.

 **A.N Hope you liked the intro. It was pretty much a summary in my opinion. Normally I wouldn't write a god like Naruto and he isn't yet. Kurama will remain uncooperative and so I balanced him out with the rinnengan. I like the idea of having Naruto create peace through a similar way the Sage of the Six paths did and I hope to create a deep plot but I don't know yet. My conversations are kinda bad in my opinion so I hope to get some reviews on them! See ya around! - Ceasare**


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